X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStockholmFile.java;h=ff2b4fafb51648c39ac166bd8fc0b393d670306f;hb=11fa2109fa963fbd910cb127f9161132ec97b9bf;hp=c6a3ce45de40c57b60d99d4a81c8968de9c01dbf;hpb=b13f4cb3250a7cb9b6cc74e51db50c01477b647f;p=jalview.git diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java index c6a3ce4..ff2b4fa 100644 --- a/src/jalview/io/StockholmFile.java +++ b/src/jalview/io/StockholmFile.java @@ -45,20 +45,21 @@ public class StockholmFile extends AlignFile { // static Logger logger = Logger.getLogger("jalview.io.StockholmFile"); StringBuffer out; // output buffer + AlignmentI al; - + public StockholmFile() { } /** - * Creates a new StockholmFile object for output. - */ + * Creates a new StockholmFile object for output. + */ public StockholmFile(AlignmentI al) { this.al = al; } - + public StockholmFile(String inFile, String type) throws IOException { super(inFile, type); @@ -144,7 +145,7 @@ public class StockholmFile extends AlignFile { // End of the alignment, pass stuff back this.noSeqs = seqs.size(); - + String propety = null; Regex pf = new Regex("PF[0-9]{5}(.*)"); // Finds AC for Pfam Regex rf = new Regex("RF[0-9]{5}(.*)"); // Finds AC for Rfam @@ -157,7 +158,7 @@ public class StockholmFile extends AlignFile } else if (rf.search(dbType)) { - propety = "RFAM"; + propety = "RFAM"; } } // logger.debug("Number of sequences: " + this.noSeqs); @@ -202,9 +203,7 @@ public class StockholmFile extends AlignFile String desc = (String) accAnnotations.get("DE"); seqO.setDescription((desc == null) ? "" : desc); } - - - + // Add DB References (if any) if (accAnnotations != null && accAnnotations.containsKey("DR")) { @@ -214,10 +213,11 @@ public class StockholmFile extends AlignFile String src = dbr.substring(0, dbr.indexOf(";")); String acn = dbr.substring(dbr.indexOf(";") + 1); jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn); - } + } } - - if (accAnnotations != null && accAnnotations.containsKey("AC") && propety != null) + + if (accAnnotations != null && accAnnotations.containsKey("AC") + && propety != null) { String dbr = (String) accAnnotations.get("AC"); if (dbr != null) @@ -225,10 +225,9 @@ public class StockholmFile extends AlignFile String src = propety; String acn = dbr.toString(); jalview.util.DBRefUtils.parseToDbRef(seqO, src, "0", acn); - } + } } - - + Hashtable features = null; // We need to adjust the positions of all features to account for gaps try @@ -253,22 +252,24 @@ public class StockholmFile extends AlignFile // TODO: map coding region to core jalview feature types String type = i.nextElement().toString(); Hashtable content = (Hashtable) features.remove(type); - + // add alignment annotation for this feature String key = type2id(type); - if (key != null) + if (key != null) { - if (accAnnotations != null && accAnnotations.containsKey(key)) + if (accAnnotations != null + && accAnnotations.containsKey(key)) { - Vector vv = (Vector) accAnnotations.get(key); + Vector vv = (Vector) accAnnotations.get(key); for (int ii = 0; ii < vv.size(); ii++) { - AlignmentAnnotation an = (AlignmentAnnotation) vv.elementAt(ii); - seqO.addAlignmentAnnotation(an); - } + AlignmentAnnotation an = (AlignmentAnnotation) vv + .elementAt(ii); + seqO.addAlignmentAnnotation(an); + } } } - + Enumeration j = content.keys(); while (j.hasMoreElements()) { @@ -577,12 +578,13 @@ public class StockholmFile extends AlignFile convert1 = openparen.replaceAll(annots); convert2 = closeparen.replaceAll(convert1); annots = convert2; - + String type = label; - if (label.contains("_cons")) { - type = (label.indexOf("_cons") == label.length() - 5) ? label - .substring(0, label.length() - 5) : label; - } + if (label.contains("_cons")) + { + type = (label.indexOf("_cons") == label.length() - 5) ? label + .substring(0, label.length() - 5) : label; + } boolean ss = false; type = id2type(type); if (type.equals("secondary structure")) @@ -648,192 +650,211 @@ public class StockholmFile extends AlignFile } return annot; } - + public String print(SequenceI[] s) { - // find max length of id - int max = 0; - int maxid = 0; - int in = 0; - Hashtable dataRef = null; - while ((in < s.length) && (s[in] != null)) - { - String tmp = printId(s[in]); - if (s[in].getSequence().length > max) - { - max = s[in].getSequence().length; - } - - if (tmp.length() > maxid) - { - maxid = tmp.length(); - } - if (s[in].getDBRef() != null) - { - for (int idb = 0; idb < s[in].getDBRef().length; idb++) - { - if (dataRef == null) - dataRef = new Hashtable(); - - String datAs1 = s[in].getDBRef()[idb].getSource().toString() + " ; " +s[in].getDBRef()[idb].getAccessionId().toString(); - dataRef.put(tmp, datAs1); + // find max length of id + int max = 0; + int maxid = 0; + int in = 0; + Hashtable dataRef = null; + while ((in < s.length) && (s[in] != null)) + { + String tmp = printId(s[in]); + if (s[in].getSequence().length > max) + { + max = s[in].getSequence().length; + } + + if (tmp.length() > maxid) + { + maxid = tmp.length(); + } + if (s[in].getDBRef() != null) + { + for (int idb = 0; idb < s[in].getDBRef().length; idb++) + { + if (dataRef == null) + dataRef = new Hashtable(); + + String datAs1 = s[in].getDBRef()[idb].getSource().toString() + + " ; " + + s[in].getDBRef()[idb].getAccessionId().toString(); + dataRef.put(tmp, datAs1); + } + } + in++; + } + maxid += 9; + int i = 0; + + // output database type + if (al.getProperties() != null) + { + if (!al.getProperties().isEmpty()) + { + Enumeration key = al.getProperties().keys(); + Enumeration val = al.getProperties().elements(); + while (key.hasMoreElements()) + { + out.append("#=GF " + key.nextElement() + " " + val.nextElement()); + out.append(newline); + } + } + } + + // output database accessions + if (dataRef != null) + { + Enumeration en = dataRef.keys(); + while (en.hasMoreElements()) + { + Object idd = en.nextElement(); + String type = (String) dataRef.remove(idd); + out.append(new Format("%-" + (maxid - 2) + "s").form("#=GS " + + idd.toString() + " ")); + if (type.contains("PFAM") || type.contains("RFAM")) + { + + out.append(" AC " + type.substring(type.indexOf(";") + 1)); + } + else + { + out.append(" DR " + type + " "); + } + out.append(newline); + } + } + + // output annotations + while (i < s.length && s[i] != null) + { + if (s[i].getDatasetSequence() != null) + { + SequenceI ds = s[i].getDatasetSequence(); + AlignmentAnnotation[] alAnot; + Annotation[] ann; + Annotation annot; + alAnot = s[i].getAnnotation(); + String feature = ""; + if (alAnot != null) + { + for (int j = 0; j < alAnot.length; j++) + { + if (ds.getSequenceFeatures() != null) + { + feature = ds.getSequenceFeatures()[0].type; + } + String key = type2id(feature); + + if (key == null) + continue; + + // out.append("#=GR "); + out.append(new Format("%-" + maxid + "s").form("#=GR " + + printId(s[i]) + " " + key + " ")); + ann = alAnot[j].annotations; + String seq = ""; + for (int k = 0; k < ann.length; k++) + { + annot = ann[k]; + String ch = (annot == null) ? Character.toString(s[i] + .getCharAt(k)) : annot.displayCharacter; + if (ch.length() == 0) + { + if (key.equals("SS")) + { + char ll = annot.secondaryStructure; + seq = (Character.toString(ll).equals(" ")) ? seq + "C" + : seq + ll; + } + else + { + seq += "."; + } + } + else if (ch.length() == 1) + { + seq += ch; + } + else if (ch.length() > 1) + { + seq += ch.charAt(1); + } } + out.append(seq); + out.append(newline); } - in++; - } - maxid += 9; - int i = 0; - - // output database type - if (al.getProperties() != null) - { - if (!al.getProperties().isEmpty()) - { - Enumeration key = al.getProperties().keys(); - Enumeration val = al.getProperties().elements(); - while (key.hasMoreElements()) - { - out.append("#=GF " + key.nextElement() + " " + val.nextElement()); - out.append(newline); - } - } - } - - // output database accessions - if (dataRef != null) - { - Enumeration en = dataRef.keys(); - while (en.hasMoreElements()) - { - Object idd = en.nextElement(); - String type = (String) dataRef.remove(idd); - out.append(new Format("%-" + (maxid - 2) + "s").form("#=GS " +idd.toString() + " ")); - if (type.contains("PFAM") || type.contains("RFAM") ) - { - - out.append(" AC " + type.substring(type.indexOf(";") + 1)); - } else - { - out.append(" DR " + type + " "); - } - out.append(newline); - } - } - - // output annotations - while (i < s.length && s[i] != null) - { - if (s[i].getDatasetSequence() != null) - { - SequenceI ds = s[i].getDatasetSequence(); - AlignmentAnnotation[] alAnot; - Annotation[] ann; - Annotation annot; - alAnot = s[i].getAnnotation(); - String feature = ""; - if (alAnot != null) - { - for (int j = 0; j < alAnot.length; j++) - { - if (ds.getSequenceFeatures() != null) - { - feature = ds.getSequenceFeatures()[0].type; - } - String key = type2id(feature); - - - if (key == null) - continue; - - // out.append("#=GR "); - out.append(new Format("%-" + maxid + "s").form("#=GR " + printId(s[i]) + " " + key + " ")); - ann = alAnot[j].annotations; - String seq = ""; - for (int k = 0; k < ann.length; k++) - { - annot = ann[k]; - String ch = (annot == null) ? Character.toString(s[i].getCharAt(k)) : annot.displayCharacter; - if (ch.length() == 0) - { - if (key.equals("SS")) { - char ll = annot.secondaryStructure; - seq = (Character.toString(ll).equals(" ")) ? seq + "C" : seq + ll; - } else { - seq += "."; - } - } else if (ch.length() == 1) { - seq += ch; - } else if (ch.length() > 1) { - seq += ch.charAt(1) ; - } - } - out.append(seq); - out.append(newline); - } - } - } - - out.append(new Format("%-" + maxid + "s").form(printId(s[i])+" ")); - out.append(s[i].getSequenceAsString()); - out.append(newline); - i++; - } - - // alignment annotation - AlignmentAnnotation aa; - if (al.getAlignmentAnnotation() != null) - { - for (int ia = 0; ia < al.getAlignmentAnnotation().length; ia++) - { - aa = al.getAlignmentAnnotation()[ia]; - if (aa.autoCalculated || !aa.visible) - { - continue; - } - String seq = ""; - String label; - - if (aa.label.equals("seq")) - label = "seq_cons"; - else - label = type2id(aa.label.toLowerCase())+"_cons"; - - if (label == null) - label = aa.label; - - out.append(new Format("%-" + maxid + "s").form("#=GC " + label+" ")); - for (int j = 0; j < aa.annotations.length; j++) - { - String ch = (aa.annotations[j] == null) ? "-" : aa.annotations[j].displayCharacter ; - if (ch.length() == 0) - { - char ll = aa.annotations[j].secondaryStructure; - if (Character.toString(ll).equals(" ")) - seq += "C"; - else - seq += ll; - } else if (ch.length() == 1) { - seq += ch; - } else if (ch.length() > 1) { - seq += ch.charAt(1) ; - } - } - out.append(seq); - out.append(newline); - } - } - return out.toString(); + } + } + + out.append(new Format("%-" + maxid + "s").form(printId(s[i]) + " ")); + out.append(s[i].getSequenceAsString()); + out.append(newline); + i++; + } + + // alignment annotation + AlignmentAnnotation aa; + if (al.getAlignmentAnnotation() != null) + { + for (int ia = 0; ia < al.getAlignmentAnnotation().length; ia++) + { + aa = al.getAlignmentAnnotation()[ia]; + if (aa.autoCalculated || !aa.visible) + { + continue; + } + String seq = ""; + String label; + + if (aa.label.equals("seq")) + label = "seq_cons"; + else + label = type2id(aa.label.toLowerCase()) + "_cons"; + + if (label == null) + label = aa.label; + + out.append(new Format("%-" + maxid + "s").form("#=GC " + label + + " ")); + for (int j = 0; j < aa.annotations.length; j++) + { + String ch = (aa.annotations[j] == null) ? "-" + : aa.annotations[j].displayCharacter; + if (ch.length() == 0) + { + char ll = aa.annotations[j].secondaryStructure; + if (Character.toString(ll).equals(" ")) + seq += "C"; + else + seq += ll; + } + else if (ch.length() == 1) + { + seq += ch; + } + else if (ch.length() > 1) + { + seq += ch.charAt(1); + } + } + out.append(seq); + out.append(newline); + } + } + return out.toString(); } public String print() { - out = new StringBuffer(); - out.append("# STOCKHOLM 1.0"); - out.append(newline); + out = new StringBuffer(); + out.append("# STOCKHOLM 1.0"); + out.append(newline); print(getSeqsAsArray()); - + out.append("//"); - out.append(newline); + out.append(newline); return out.toString(); } @@ -872,25 +893,25 @@ public class StockholmFile extends AlignFile + id); return id; } - + protected static String type2id(String type) { - String key = null; - Enumeration e = typeIds.keys(); - while (e.hasMoreElements()) - { - Object ll = e.nextElement(); - if (typeIds.get(ll).toString().equals(type)) - { - key = (String) ll; - break; - } - } - if (key != null) + String key = null; + Enumeration e = typeIds.keys(); + while (e.hasMoreElements()) + { + Object ll = e.nextElement(); + if (typeIds.get(ll).toString().equals(type)) { - return (String) key; + key = (String) ll; + break; } - System.err.println("Warning : Unknown Stockholm annotation type: " + } + if (key != null) + { + return (String) key; + } + System.err.println("Warning : Unknown Stockholm annotation type: " + type); return key; }